MOLECULAR DYNAMIC SIMULATION OF BACTERIORHODOPSIN IN DIMYRISTOYLPHOSPHATIDYLCHOLINE BILAYER MEMBRANE

• Main Author: Khumaini, Khabib
• Format: Theses
• Language: Indonesia
• Subjects: Kimia
• Online Access: https://digilib.itb.ac.id/gdl/view/34955
• Institution: Institut Teknologi Bandung

Bacteriorhodopsin is a membrane protein with a special function to transport pro- tons from intracellular to extracellular site of the membrane cell. The protons trans- port facilitated by this protein is an endergonics process since its direction is against the protons concentration gradient. Unlike typical transporter proteins, bacterio- rhodopsin is a relatively small protein comprising only a single subunit constructed with 248 amino acid residues. Mechanisms and kinetics of protons transport facili- tated by this protein has been widely studied experimentally, i.e. X-ray diffraction, UV-VIS, and FT-IR techniques. In addition, theoretical studies with the approach of ab-initio and hybrid Quantum Mechanic-Molecular Mechanic (QMMM) calcula- tions have been devised to explain the mechanisms of retinal lysine isomerization in bacteriorhodopsin under the light irradiation. Nevertheless, the detail of the protons tranport via this protein including its energy change following the process has not been clearly explained. In addition, the dynamics and stability of bacteriorhodopsin under various solvent system as water, membrane-water and membrane-water-salt systems have not yet been investigated. The objective of the present study, there- fore, is to investigate the stability of bacteriorhodopsin in various solvent systems mentioned above and to elucidate detail mechanisms of proton transport and its en- ergy changes at atomic level with molecular dynamics simulations. This work is performed by three stages i.e. constructions of model structures, molecular dynamic (MD) simulations, and the analysis of simulation trajectories. The first stage includes trans and cis retinal lysine parameterizations, lipid DMPC (dimyristoylphosphatidylcholine) united atom parameterizations, structural improve- ment of bacteriorhodopsin with MODELLER and bilayer constructions using Pack- mol. At the second stage, all MD simulations were undertaken using PMEMD mod- ule of AMBER10 simulation package under NPT ensemble, i.e. 310 K and 1 atm. MD simulations at various solvent systems were performed for 10 ns in the water, 20 ns in the water and bilayer membrane, and 10 ns in the salt solution and bilayer membrane. The salt concentrations were set to 3 M NaCl and 1 M KCl at extra and intracellular parts, respectively. RMSD analysis to the recorded simulation trajectories showed that there were no major differences in terms of the stability of bacteriorhodopsin in all of the three sol- vent models. The apparent stability was likely due to the small size of the protein and its major helical structures. In terms of RMSF analysis, however, we observed the prominent internal dynamics at the particular region of the protein immersed in the lipid membrane under high salt concentration. At this condition, the flexibility of ?-sheet segment of the protein that directly in contact with 3 M NaCl solution, reduced significantly compared to that in the water only system. It is likely to occur due to the solvation competition between salt and the protein causing the reo- rentation of the hidrophobic residues within the beta-sheet segment. Our structural inspections to DMPC bilayer membrane found that the lipid bilayer was apparently more dense and thicker at high salt concentration than those at the absence of the salt. Energetic analysis to the mechanism of the proton transport process found that the isomerization of retinal lysine and proton transfer from Glu194 to the extracellular water was an endergonic process. In contrast, the proton transfer from retinal lysine to Asp85 was an exergonics process. The next stages of the proton transfer was not successfully simulated since it requires to model very complex hydrogen bonds network in order to successfully transfer the protein from Asp96 to retinal lysine. The complexity of the process and the energy barrier in each stages are reflected by the time required to pass each stages that ranges from 1 µs to 5 ms, which is too expensive to be achieved with the current method of the molecular dynamics simulations.